fix(db): close SQLite connections explicitly to suppress ResourceWarning on Python 3.13

`sqlite3.Connection.__exit__` only commits/rolls back a transaction — it
does not close the connection. Python 3.13 (the Nix env on the KVM
runner) emits `ResourceWarning: unclosed database` for every connection
GC'd without an explicit close, producing noisy output in the coverage job.

Add `DbStore._connection()`, a `contextmanager` that calls `self._connect()`,
wraps it in the existing transaction context manager, and closes the
connection in a `finally` block. Change all `with self._connect() as conn:`
call sites in `db_store.py`, `audit_store.py`, `queue_store.py`, and
`orchestrator/registry.py` to `with self._connection() as conn:`.
`_connect()` remains as the per-subclass hook (RegistryStore overrides
it to set `busy_timeout`); `_connection()` delegates to `self._connect()` so
the override is respected.

bot_bottle/audit_store.py

@@ -42,7 +42,7 @@ class AuditStore(DbStore):
         super().__init__(db_path or host_db_path(), migrations)
 
     def write_audit_entry(self, entry: AuditEntry) -> Path:
-        with self._connect() as conn:
+        with self._connection() as conn:
             conn.execute(
                 """
                 INSERT INTO supervise_audit_entries (
@@ -66,7 +66,7 @@ class AuditStore(DbStore):
     def read_audit_entries(self, component: str, slug: str) -> list[AuditEntry]:
         if not self.db_path.is_file():
             return []
-        with self._connect() as conn:
+        with self._connection() as conn:
             rows = conn.execute(
                 """
                 SELECT * FROM supervise_audit_entries

bot_bottle/db_store.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import sqlite3
+from contextlib import contextmanager
 from pathlib import Path
 
 try:
@@ -28,12 +29,21 @@ class DbStore:
         conn.row_factory = sqlite3.Row
         return conn
 
+    @contextmanager
+    def _connection(self):
+        conn = self._connect()
+        try:
+            with conn:
+                yield conn
+        finally:
+            conn.close()
+
     def is_migrated(self) -> bool:
         """Return True if the DB is fully up-to-date, False if migration is needed."""
         if not self.db_path.exists():
             return False
         try:
-            with self._connect() as conn:
+            with self._connection() as conn:
                 row = conn.execute(
                     "SELECT version FROM schema_versions WHERE module = ?",
                     (self._migrations.schema_key,),
@@ -45,7 +55,7 @@ class DbStore:
 
     def migrate(self) -> None:
         """Apply any pending migrations and set permissions on the DB file."""
-        with self._connect() as conn:
+        with self._connection() as conn:
             self._migrations.apply(conn)
         self._chmod()
 

bot_bottle/orchestrator/registry.py

@@ -167,7 +167,7 @@ class RegistryStore(DbStore):
             metadata=metadata,
             policy=policy,
         )
-        with self._connect() as conn:
+        with self._connection() as conn:
             conn.execute(
                 "DELETE FROM orchestrator_bottles "
                 "WHERE source_ip = ? AND state = 'active' AND bottle_id != ?",
@@ -193,7 +193,7 @@ class RegistryStore(DbStore):
     def set_policy(self, bottle_id: str, policy: str) -> bool:
         """Update a bottle's policy in place (live reload). Returns True if
         the bottle exists."""
-        with self._connect() as conn:
+        with self._connection() as conn:
             cur = conn.execute(
                 "UPDATE orchestrator_bottles SET policy = ? WHERE bottle_id = ?",
                 (policy, bottle_id),
@@ -203,7 +203,7 @@ class RegistryStore(DbStore):
 
     def deregister(self, bottle_id: str) -> bool:
         """Remove a bottle. Returns True if a row was deleted."""
-        with self._connect() as conn:
+        with self._connection() as conn:
             cur = conn.execute(
                 "DELETE FROM orchestrator_bottles WHERE bottle_id = ?", (bottle_id,)
             )
@@ -211,7 +211,7 @@ class RegistryStore(DbStore):
 
     def get(self, bottle_id: str) -> BottleRecord | None:
         """Return the bottle by id, or None if absent."""
-        with self._connect() as conn:
+        with self._connection() as conn:
             row = conn.execute(
                 "SELECT * FROM orchestrator_bottles WHERE bottle_id = ?", (bottle_id,)
             ).fetchone()
@@ -219,7 +219,7 @@ class RegistryStore(DbStore):
 
     def all(self) -> list[BottleRecord]:
         """Every registered bottle, oldest first."""
-        with self._connect() as conn:
+        with self._connection() as conn:
             rows = conn.execute(
                 "SELECT * FROM orchestrator_bottles ORDER BY created_at"
             ).fetchall()
@@ -232,7 +232,7 @@ class RegistryStore(DbStore):
         source IP is unspoofable (Firecracker `/31` + nft) and the control
         plane is reachable only by the trusted gateway; pair with the
         identity token (`attribute`) elsewhere."""
-        with self._connect() as conn:
+        with self._connection() as conn:
             rows = conn.execute(
                 "SELECT * FROM orchestrator_bottles "
                 "WHERE source_ip = ? AND state = 'active'",

bot_bottle/queue_store.py

@@ -66,7 +66,7 @@ class QueueStore(DbStore):
         super().__init__(resolved, migrations)
 
     def write_proposal(self, proposal: Proposal) -> Path:
-        with self._connect() as conn:
+        with self._connection() as conn:
             conn.execute(
                 """
                 INSERT OR REPLACE INTO supervise_proposals (
@@ -89,7 +89,7 @@ class QueueStore(DbStore):
         return self.db_path
 
     def read_proposal(self, proposal_id: str) -> Proposal:
-        with self._connect() as conn:
+        with self._connection() as conn:
             row = conn.execute(
                 """
                 SELECT * FROM supervise_proposals
@@ -104,7 +104,7 @@ class QueueStore(DbStore):
     def list_pending_proposals(self) -> list[Proposal]:
         if not self.db_path.is_file():
             return []
-        with self._connect() as conn:
+        with self._connection() as conn:
             rows = conn.execute(
                 """
                 SELECT p.* FROM supervise_proposals p
@@ -125,7 +125,7 @@ class QueueStore(DbStore):
     def list_all_pending_proposals(self) -> list[Proposal]:
         if not self.db_path.is_file():
             return []
-        with self._connect() as conn:
+        with self._connection() as conn:
             rows = conn.execute(
                 """
                 SELECT p.* FROM supervise_proposals p
@@ -142,7 +142,7 @@ class QueueStore(DbStore):
         return [self._row_to_proposal(row) for row in rows]
 
     def write_response(self, response: Response) -> Path:
-        with self._connect() as conn:
+        with self._connection() as conn:
             conn.execute(
                 """
                 INSERT OR REPLACE INTO supervise_responses (
@@ -161,7 +161,7 @@ class QueueStore(DbStore):
         return self.db_path
 
     def read_response(self, proposal_id: str) -> Response:
-        with self._connect() as conn:
+        with self._connection() as conn:
             row = conn.execute(
                 """
                 SELECT * FROM supervise_responses
@@ -176,7 +176,7 @@ class QueueStore(DbStore):
     def archive_proposal(self, proposal_id: str) -> None:
         if not self.db_path.is_file():
             return
-        with self._connect() as conn:
+        with self._connection() as conn:
             conn.execute(
                 """
                 UPDATE supervise_proposals SET archived = 1